It's a case by case basis. Some have been firmly a part of the modern Treklit continuity, such as Wildstorm's TNG/DS9 crossover, "Divided We Fall", some have used elements of modern Treklit, such as the Andorian four-partner paradigm in IDW's "Alien Spotlight: Andorians", and sometimes Treklit has adopted elements from the comics, such as the events of WildStorm's "The Gorn Crisis" and Andorian President Thelian, of "Enter the Wolves", being referenced in "Titan: Taking Wing" and "Articles of the Federation".

So far, Braga's Borg story seems to be a possible future type of thing.